[gmx-users] pdb2gmx -water-> grompp; grompp error
Paymon Pirzadeh
ppirzade at ucalgary.ca
Tue Aug 25 21:58:27 CEST 2009
When I look at the .top file generated by pdb2gmx, the last lines show
how this -0.99 is generated:
442 opls_302 37 ARG CZ 138 0.64 12.011 ;
qtot -0.33
443 opls_300 37 ARG NH1 139 -0.8 14.0067 ;
qtot -1.13
444 opls_301 37 ARG HH11 139 0.46 1.008 ;
qtot -0.67
445 opls_301 37 ARG HH12 139 0.46 1.008 ;
qtot -0.21
446 opls_300 37 ARG NH2 140 -0.8 14.0067 ;
qtot -1.01
447 opls_301 37 ARG HH21 140 0.46 1.008 ;
qtot -0.55
448 opls_301 37 ARG HH22 140 0.46 1.008 ;
qtot -0.09
449 opls_271 37 ARG C 141 0.7 12.011 ;
qtot 0.61
450 opls_272 37 ARG O1 141 -0.8 15.9994 ;
qtot -0.19
451 opls_272 37 ARG O2 141 -0.8 15.9994 ;
qtot -0.99
The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
simulation is supposed to be close to 7.0, I believe one of the
negatively-charged side chains needs to be neutralized. That's why I
think one Na+ might be helpful.
Payman
On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:
>
> Paymon Pirzadeh wrote:
> > OK! It worked! Thanks a lot again. But I have a final technical
> > question. After running grompp, it shows that my box has a net charge of
> > -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
> > OK?! or even this 0.01 charge will cause me troubles?
>
> Depending on the size of your system, rounding errors can occur. It is unusual
> that the hundredths place would be showing this error. Usually you'd get
> something like 0.99998 or something. Your water topology has a zero net charge;
> is there something else in your system causing the -1 charge?
>
> Adding a single Na+ to neutralize the charge may be appropriate, but that's up
> to you based on what's in your system (something else may be broken, but I just
> don't know).
>
> -Justin
>
> > Sorry for tons of e-mails.
> > regards,
> >
> > Payman
> >
> >
> > On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> OK! That's fine. But what if I do not have permissions to make such
> >>> changes in the itp files? Also, isn't that the case that when you define
> >> That's why I said copy the force field files into your local directory. Once
> >> there, you can modify them.
> >>
> >>> sth for the second time, grompp will take the second one? Sorry for mass
> >>> of e-mail!
> >>>
> >> That is only true in the case of .mdp files.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
> >>>> Paymon Pirzadeh wrote:
> >>>>> I have done that already! I use my local copy to make my files. but how
> >>>>> can I get rid of this error? get into the oplsaanb.itp or include this
> >>>>> water model in the topology file before oplsaa.itp?
> >>>>>
> >>>> I don't understand what you're saying you've already done.
> >>>>
> >>>> The problem is this: when grompp attempts to assemble the .tpr file, it reads
> >>>> all of the information from the ffoplsaa*.itp files. It finds the directives
> >>>> like [defaults], [atomtypes], etc in a pre-defined order. If, later, it finds a
> >>>> duplicate of these directives, it complains. So when you #include your .itp
> >>>> file with new [atomtypes], it generates the error because it is a duplicate
> >>>> directive. You have to include the new atom types in ffoplsaanb.itp in the
> >>>> [atomtypes] directive of this file. The rest of the topology shouldn't cause a
> >>>> problem, just the [atomtypes] directive.
> >>>>
> >>>> -Justin
> >>>>
> >>>>> Payman
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
> >>>>>> Paymon Pirzadeh wrote:
> >>>>>>> OK!
> >>>>>>> here is the .itp file which I generated. I might upload it because it
> >>>>>>> has passed the initial tests.
> >>>>>>>
> >>>>>>> ; This is an itp file to describe water's six-site model by H. Nada and
> >>>>>>> J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
> >>>>>>> (2003)
> >>>>>>> ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
> >>>>>>> and 3 Coulomb sites
> >>>>>>> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
> >>>>>>> 111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
> >>>>>>>
> >>>>>>> [ defaults ]
> >>>>>>> ; non-bondedtype combrule genpairs FudgeLJ
> >>>>>>> FudgeQQ N
> >>>>>>> 1 2 NO
> >>>>>>>
> >>>>>>> [ atomtypes ]
> >>>>>>> ;name mass charge ptype c6 c12
> >>>>>>> OW 15.9994 0.0 A 0.3115 0.714845562
> >>>>>>> HW 1.00800 0.477 A 0.0673 0.11541
> >>>>>>> MW 0.000 -0.866 D 0.00 0.00
> >>>>>>> LW 0.00 -0.044 D 0.00 0.00
> >>>>>>>
> >>>>>>> [ moleculetype ]
> >>>>>>> ;molname nrexcl
> >>>>>>> SOL 2
> >>>>>>>
> >>>>>>> [ atoms ]
> >>>>>>> ; nr atomtype resnr residuename atom cgnr charge
> >>>>>>> 1 OW 1 SOL OW 1 0.0
> >>>>>>> 2 HW 1 SOL HW1 1 0.477
> >>>>>>> 3 HW 1 SOL HW2 1 0.477
> >>>>>>> 4 MW 1 SOL MW 1 -0.866
> >>>>>>> 5 LW 1 SOL LP1 1 -0.044
> >>>>>>> 6 LW 1 SOL LP2 1 -0.044
> >>>>>>>
> >>>>>>> [ settles ]
> >>>>>>> ; OW function doh dhh
> >>>>>>> 1 1 0.0980 0.15856
> >>>>>>>
> >>>>>>> [ dummies3 ]
> >>>>>>> ; These set of parameters are for M site which can be easily calculated
> >>>>>>> using TIP4P calculations from tip4p.itp
> >>>>>>> ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
> >>>>>>> b*(r(i)-r(k))
> >>>>>>> ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
> >>>>>>> Remember that OM is in the same direction of OH bonds.
> >>>>>>> ; Remember this site is in the same plane of OH bonds; so, its function
> >>>>>>> 1
> >>>>>>> ;
> >>>>>>> ; site from function a b
> >>>>>>> 4 1 2 3 1 0.199642536 0.199642536
> >>>>>>>
> >>>>>>> ; Now we define the position of L sites which can be obtained from
> >>>>>>> tip5p.itp
> >>>>>>> ; So, it will be described as dummy site 3out: r(v) = r(i) +
> >>>>>>> a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
> >>>>>>> ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
> >>>>>>> |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
> >>>>>>> bonds, a minus sign is added. This part is similar to M site.
> >>>>>>> ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
> >>>>>>> the magnitude of vector product of OH bonds.
> >>>>>>> ; This sites are tetrahedral sites; so, its function 4
> >>>>>>> ;
> >>>>>>> ; site from function a b
> >>>>>>> c
> >>>>>>> 5 1 2 3 4 -0.437172388 -0.437172388
> >>>>>>> 8.022961206
> >>>>>>> 6 1 2 3 4 -0.437172388 -0.437172388
> >>>>>>> -8.022961206
> >>>>>>>
> >>>>>>> [ exclusions ]
> >>>>>>> 1 2 3 4 5 6
> >>>>>>> 2 1 3 4 5 6
> >>>>>>> 3 1 2 4 5 6
> >>>>>>> 4 1 2 3 5 6
> >>>>>>> 5 1 2 3 4 6
> >>>>>>> 6 1 2 3 4 5
> >>>>>>>
> >>>>>>> and here is the message I get from grompp:
> >>>>>>>
> >>>>>>> Program grompp_d_mpi, VERSION 4.0.5
> >>>>>>> Source code file: topio.c, line: 415
> >>>>>>>
> >>>>>>> Fatal error:
> >>>>>>> Syntax error - File sixsitewater.itp, line 12
> >>>>>>> Last line read:
> >>>>>>> '[ atomtypes ]'
> >>>>>>> Invalid order for directive atomtypes
> >>>>>>> -------------------------------------------------------
> >>>>>>>
> >>>>>>> I believe the original files of GROMACS need admin permissions which I
> >>>>>>> do not have on the cluster that I am currently using and I am not sure
> >>>>>>> if that might not cause troubles for other users. So, I thought how I
> >>>>>>> can keep the changes local.
> >>>>>>>
> >>>>>> Make a copy in your local directory; grompp will use these before looking for
> >>>>>> system-wide files. As a general rule, whenever developing new parameters or
> >>>>>> adjusting files, do so locally before potentially messing yourself (or others) up :)
> >>>>>>
> >>>>>> -Justin
> >>>>>>
> >>>>>>> Payman
> >>>>>>>
> >>>>>>>
> >>>>>>> On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:
> >>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>> Hello,
> >>>>>>>>> Just a reminder that I had troubled with combination rules between my
> >>>>>>>>> water model and GROMACS forcefields. I fixed the problem by adjusting my
> >>>>>>>>> water model's parameters. BUT, now, I specified the new parameters in
> >>>>>>>>> my .itp file under [ atomtype ] category and grompp makes errors out of
> >>>>>>>>> the orders. Now I am using OPLSaa. I suspect again the problem comes
> >>>>>>>>> from the presence of the second [atomtype ]. How can I keep my new
> >>>>>>>>> parameters and use them in my water model's itp file? Or should I change
> >>>>>>>>> these parameters in the OPLSaa.itp file?
> >>>>>>>> You can't have a second [atomtypes] directive. You can add new parameters to
> >>>>>>>> ffoplsaanb.itp to account for the atom types you are implementing, though.
> >>>>>>>>
> >>>>>>>> If you want anything more specific, you'll probably have to provide the topology
> >>>>>>>> file you're working with, as well as any actual error messages you're seeing.
> >>>>>>>>
> >>>>>>>> -Justin
> >>>>>>>>
> >>>>>>>>> Regards,
> >>>>>>>>>
> >>>>>>>>> Payman
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:
> >>>>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>>>> I checked all the force-fields available in the GROAMCS. None of them
> >>>>>>>>>>> have the #2 combination rule which matches my water model! Any
> >>>>>>>>>>> alternatives (rather than changing my water model)?
> >>>>>>>>>> A water model that isn't compatible with the model of the solutes isn't
> >>>>>>>>>> of any value, so it looks like you have put the cart before the horse.
> >>>>>>>>>>
> >>>>>>>>>> Mark
> >>>>>>>>>>
> >>>>>>>>>>> On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote:
> >>>>>>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>>>>>> That was very helpful! But I realized a problem. The OPLSaa uses the
> >>>>>>>>>>>>> combination rule #3 in [ defaults ] while my water model uses #2. Now if
> >>>>>>>>>>>>> I comment out my water model's combination, I am not sure what I am
> >>>>>>>>>>>>> going to face! Any comments?
> >>>>>>>>>>>>>
> >>>>>>>>>>>> Then I would say that your water model's combination rule is inconsistent with
> >>>>>>>>>>>> the method of nonbonded calculations in OPLS. It appears that the only
> >>>>>>>>>>>> difference between combination rules 2 and 3 comes when a specific interaction
> >>>>>>>>>>>> is not defined in the [nonbond_params] section. The specifics of these
> >>>>>>>>>>>> combination rules are given in manual section 5.3.3.
> >>>>>>>>>>>>
> >>>>>>>>>>>> -Justin
> >>>>>>>>>>>>
> >>>>>>>>>>>>> Payman
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On Tue, 2009-08-18 at 18:19 -0400, Justin A. Lemkul wrote:
> >>>>>>>>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>>>>>>>> Well,
> >>>>>>>>>>>>>>> I changed the topology file of the system and manually typed the .itp of
> >>>>>>>>>>>>>>> my own water model. Just a reminder that I have used my own water
> >>>>>>>>>>>>>>> model's .itp file successfully in pure water systems. This .itp file
> >>>>>>>>>>>>>>> starts from [ defaults ] and contains all information needed. But when
> >>>>>>>>>>>>>>> it comes to grompp, the following error appears:
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Program grompp_d_mpi, VERSION 4.0.5
> >>>>>>>>>>>>>>> Source code file: topio.c, line: 415
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Fatal error:
> >>>>>>>>>>>>>>> Syntax error - File sixsitewater.itp, line 6
> >>>>>>>>>>>>>>> Last line read:
> >>>>>>>>>>>>>>> '[ defaults ]'
> >>>>>>>>>>>>>>> Invalid order for directive defaults
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>> The only time that [defaults] should appear is in the force field that you are
> >>>>>>>>>>>>>> calling (i.e., ffoplsaa.itp):
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> -Justin
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> I am trying to use this water model with OPLSaa. what kind of directive
> >>>>>>>>>>>>>>> am I missing?
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Payman
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote:
> >>>>>>>>>>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>>>>>>>>>> Hello,
> >>>>>>>>>>>>>>>>> I am trying to use a different water model for my proteins (using oplsaa
> >>>>>>>>>>>>>>>>> force field). I use the .itp file which I developed, but pdb2gmx does
> >>>>>>>>>>>>>>>>> not accept it. I am a bit confused on how I can make my water model work
> >>>>>>>>>>>>>>>>> with OPLSaa. Based on what I saw from spc.itp or other samples, do I
> >>>>>>>>>>>>>>>>> need to change the names of my particles in my water .itp file by
> >>>>>>>>>>>>>>>>> including _FF_OPLS?
> >>>>>>>>>>>>>>>> I don't know how pdb2gmx decides how to recognize water models; it may be
> >>>>>>>>>>>>>>>> hard-coded. In any case, your atom types have to be consistent with OPLS
> >>>>>>>>>>>>>>>> standards; as for whether or not you need the #ifdef _FF_OPLS in your .itp file,
> >>>>>>>>>>>>>>>> you may not need it if OPLS is the only force field with which it will be used.
> >>>>>>>>>>>>>>>> The #ifdef blocks just prevent a GROMOS system from trying to recognize OPLS, etc.
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> -Justin
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> Regards,
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> Payman
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> _______________________________________________
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> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>> _______________________________________________
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> >>>>>>>>>> _______________________________________________
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> >>>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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> >>>>>>>>>
> >>>> --
> >>>> ========================================
> >>>>
> >>>> Justin A. Lemkul
> >>>> Ph.D. Candidate
> >>>> ICTAS Doctoral Scholar
> >>>> Department of Biochemistry
> >>>> Virginia Tech
> >>>> Blacksburg, VA
> >>>> jalemkul[at]vt.edu | (540) 231-9080
> >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>>>
> >>>> ========================================
> >>>> _______________________________________________
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> >>>>
> >>>>
> >>>
> >
> >
>
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